jalview

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JAL-3618 Enable appBundleIsTraversable in JFileChooser on macOS

JAL-3594 Allow a channel to use a different preferences file than .jalview_properties, with initial read from .jalview_properties

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    /src/jalview/util/ChannelProperties.java
JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog

JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog

Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"

This reverts commit cb628aab46f9027e71b71203b322f96710e09990, reversing

changes made to a40669b2eeb34a6c760b63c172a31a194b456f24.

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    /test/jalview/util/MappingUtilsTest.java
Revert "JAL-3816 release notes for JAL-3806"

This reverts commit ead40d75a04715c80c61e34e277bb995cb2bef90.

JAL-3826 added root=true to editorconfig for IntelliJ

JAL-3826 Simple configuration with CodeStyle implemented in .editorconfig file

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    /src/.editorconfig
First commit of 3DB FTS Panel & Restclient

JAL-3816 release notes for JAL-3806

Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch

JAL-3816 JAL-3814 JAL-3813 JAL-3812 JAL-3811 JAL-3818 release notes and date for 2.11.1.4 release

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no sma...

This is likely an improvement on the "roll your own" pattern of setting Runnable handlers for dialog responses as hacked together for JalviewJS (JAL-3048). If so, it would be preferable (but no small job) to change all dialogs to this pattern.

There are still numerous dialogs that have not been changed to either pattern (so won't work in SwingJS): see comment at https://issues.jalview.org/browse/?focusedCommentId=20525&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#JAL-3048comment-20525.

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

Class has some compiler warnings which could easily be resolved (typed Hashtable, unused import).

It would be good to add Javadoc to this method

It would be good to add Javadoc to this method

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

As an aside, I would suggest inlining (removing) the two overloaded constructors that call this one (to reduce code bloat).

Merge branch 'bug/JAL-3818_jmolDeadlock' into releases/Release_2_11_1_Branch

Merge branch 'releases/Release_2_11_1_4_debianpatches' into releases/Release_2_11_1_Branch

JAL-3818 process Jmol callbacks in AWT thread
JAL-3818 process Jmol callbacks in AWT thread
Merge branch 'bug/JAL-3807_jpred-with-slivka' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'bug/JAL-3809_ws_params_dialog_fix' into alpha/JAL-3066_Jalview_212_slivka-integration

Merge branch 'bug/JAL-3810_annotation_ws_stopping_abruptly' into bug/JAL-3809_ws_params_dialog_fix

Merge branch 'feature/JAL-3690_callback-based-web-services' into alpha/JAL-3066_Jalview_212_slivka-integration

JAL-3822 pass panel height and width to wrapped geometry calculations

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    /test/jalview/gui/SeqPanelTest.java
JAL-2422 remove temporary patch (requires ChimeraX Daily or 1.2 build)

JAL-3821 patch for 2.11.2 to retrieve RNA ENA records as RNA

Merge branch 'feature/JAL-3692enaEndpoint' into patch/for2.11.2/JAL-3821_ena_rna_moltype

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    /resources/lang/Messages_es.properties
JAL-3821 rough and ready patch translates t/T to u/U when mol_type includes rna